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| # Copyright 2021 DeepMind Technologies Limited | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| """Library to run HHsearch from Python.""" | |
| import glob | |
| import os | |
| import subprocess | |
| from typing import Sequence | |
| from absl import logging | |
| from alphafold.data.tools import utils | |
| # Internal import (7716). | |
| class HHSearch: | |
| """Python wrapper of the HHsearch binary.""" | |
| def __init__(self, | |
| *, | |
| binary_path: str, | |
| databases: Sequence[str], | |
| maxseq: int = 1_000_000): | |
| """Initializes the Python HHsearch wrapper. | |
| Args: | |
| binary_path: The path to the HHsearch executable. | |
| databases: A sequence of HHsearch database paths. This should be the | |
| common prefix for the database files (i.e. up to but not including | |
| _hhm.ffindex etc.) | |
| maxseq: The maximum number of rows in an input alignment. Note that this | |
| parameter is only supported in HHBlits version 3.1 and higher. | |
| Raises: | |
| RuntimeError: If HHsearch binary not found within the path. | |
| """ | |
| self.binary_path = binary_path | |
| self.databases = databases | |
| self.maxseq = maxseq | |
| for database_path in self.databases: | |
| if not glob.glob(database_path + '_*'): | |
| logging.error('Could not find HHsearch database %s', database_path) | |
| raise ValueError(f'Could not find HHsearch database {database_path}') | |
| def query(self, a3m: str) -> str: | |
| """Queries the database using HHsearch using a given a3m.""" | |
| with utils.tmpdir_manager(base_dir='/tmp') as query_tmp_dir: | |
| input_path = os.path.join(query_tmp_dir, 'query.a3m') | |
| hhr_path = os.path.join(query_tmp_dir, 'output.hhr') | |
| with open(input_path, 'w') as f: | |
| f.write(a3m) | |
| db_cmd = [] | |
| for db_path in self.databases: | |
| db_cmd.append('-d') | |
| db_cmd.append(db_path) | |
| cmd = [self.binary_path, | |
| '-i', input_path, | |
| '-o', hhr_path, | |
| '-maxseq', str(self.maxseq) | |
| ] + db_cmd | |
| logging.info('Launching subprocess "%s"', ' '.join(cmd)) | |
| process = subprocess.Popen( | |
| cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
| with utils.timing('HHsearch query'): | |
| stdout, stderr = process.communicate() | |
| retcode = process.wait() | |
| if retcode: | |
| # Stderr is truncated to prevent proto size errors in Beam. | |
| raise RuntimeError( | |
| 'HHSearch failed:\nstdout:\n%s\n\nstderr:\n%s\n' % ( | |
| stdout.decode('utf-8'), stderr[:100_000].decode('utf-8'))) | |
| with open(hhr_path) as f: | |
| hhr = f.read() | |
| return hhr | |